On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> I have a query about a failing tool test on the Tool Shed, where it
> seems Galaxy is trying to convert both the expected BAM output
> and the tool's BAM output into SAM for comparison - but this
> fails.
>
> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>
> 2015-01-27 02:13:51
> ...
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
> Stderr:
> Traceback:
> Traceback (most recent call last):
>   File 
> "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 122, in test_tool
>     self.do_it( td )
>   File 
> "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 40, in do_it
>     self._verify_outputs( testdef, test_history, jobs, shed_tool_id,
> data_list, galaxy_interactor )
>   File 
> "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 80, in _verify_outputs
>     galaxy_interactor.verify_output( history, jobs, output_data,
> output_testdef=output_testdef, shed_tool_id=shed_tool_id,
> maxseconds=maxseconds )
>   File 
> "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py",
> line 66, in verify_output
>     self.twill_test_case.verify_hid( outfile, hda_id=hid,
> attributes=attributes, dataset_fetcher=fetcher,
> shed_tool_id=shed_tool_id )
>   File 
> "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
> line 2341, in verify_hid
>     raise AssertionError( errmsg )
> AssertionError: History item  different than expected, difference (using 
> diff):
> ( 
> /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam
> v. 
> /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpExQWRD/tmpSknKqLsam_spec_padded.depad.bam
> )
> Converting local (test-data) bam to sam failed
>
> (and same error on the second test)

https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing,
although now with a more concise traceback:

Test runs
2015-01-29 02:26:31
Automated test environment
Tests that failed
Tool id: samtools_depad
Tool version: samtools_depad
Test: test_tool_000000
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
Stderr:
Traceback:
Traceback (most recent call last):
  File 
"/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 122, in test_tool
    self.do_it( td )
  File 
"/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 40, in do_it
    self._verify_outputs( testdef, test_history, jobs, shed_tool_id,
data_list, galaxy_interactor )
  File 
"/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 80, in _verify_outputs
    galaxy_interactor.verify_output( history, jobs, output_data,
output_testdef=output_testdef, shed_tool_id=shed_tool_id,
maxseconds=maxseconds )
  File 
"/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py",
line 66, in verify_output
    self.twill_test_case.verify_hid( outfile, hda_id=hid,
attributes=attributes, dataset_fetcher=fetcher,
shed_tool_id=shed_tool_id )
  File 
"/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 2341, in verify_hid
    raise AssertionError( errmsg )
AssertionError: History item  different than expected, difference (using diff):
( 
/tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam
v. 
/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpfD5MDC/tmpOpbQxNsam_spec_padded.depad.bam
)
Converting local (test-data) bam to sam failed



> The same occurs on the Test Tool Shed (with a very slightly updated
> version of this tool), although with a more concise traceback:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>
> 2015-01-25 08:21:59
> ...
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
> Stderr:
> Traceback:
> Traceback (most recent call last):
>   File 
> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 268, in test_tool
>     self.do_it( td )
>   File 
> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 67, in do_it
>     raise e
> JobOutputsError: History item  different than expected, difference (using 
> diff):
> ( 
> /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam
> v. 
> /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam
> )
> Converting local (test-data) bam to sam failed
>

https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also
still failing,

Test runs
2015-01-25 08:21:59
Automated test environment
Tests that failed
Tool id: samtools_depad
Tool version: samtools_depad
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
Stderr:
Traceback:
Traceback (most recent call last):
  File 
"/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File 
"/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 67, in do_it
    raise e
JobOutputsError: History item  different than expected, difference (using diff):
( 
/tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam
v. 
/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam
)
Converting local (test-data) bam to sam failed




> Both tests should produce a BAM file matching the provided
> test-data/sam_spec_padded.depad.bam example. The error
> comes from test/base/twilltestcase.py,
>
>         p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % (
> temp_local.name, local_name  ), shell=True )
>         assert not p.wait(), 'Converting local (test-data) bam to sam failed'
>
> Running this command locally at the terminal seems to work fine,
> both with samtools 0.1.19 and 1.1.
>
> $ ~/bin/samtools_0.1.19 view -h -o temp.sam sam_spec_padded.depad.bam
> $ more temp.sam
> @HD    VN:1.5    SO:coordinate
> @SQ    SN:ref    LN:45
> ref    516    ref    1    0    45M    *    0    0
> AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT    *
> r001    99    ref    7    30    8M2I4M1D3M    =    37    41
> TTAGATAAAGGATACTG    *
> *    768    ref    8    30    1M    *    0    0    *    *
> CT:Z:.;Warning;Note=Ref wrong?
> r002    0    ref    9    30    3S6M1P1I4M    *    0    0
> AAAAGATAAGGATA    *    PT:Z:1;4;+;homopolymer
> r003    0    ref    9    30    5H6M    *    0    0    AGCTAA    *    NM:i:1
> r004    0    ref    16    30    6M14D5M    *    0    0    ATAGCTTCAGC    *
> r003    2064    ref    29    30    6H5M    *    0    0    TAGGC    *    NM:i:0
> r001    147    ref    37    30    9M    =    7    -41    CAGCGGCAT
> *    NM:i:1
>
> $ ~/bin/samtools_1.1 view -h -o temp.sam sam_spec_padded.depad.bam
> [galaxy@ppserver test-data]$ more temp.sam
> @HD    VN:1.5    SO:coordinate
> @SQ    SN:ref    LN:45
> ref    516    ref    1    0    45M    *    0    0
> AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT    *
> r001    99    ref    7    30    8M2I4M1D3M    =    37    41
> TTAGATAAAGGATACTG    *
> *    768    ref    8    30    1M    *    0    0    *    *
> CT:Z:.;Warning;Note=Ref wrong?
> r002    0    ref    9    30    3S6M1P1I4M    *    0    0
> AAAAGATAAGGATA    *    PT:Z:1;4;+;homopolymer
> r003    0    ref    9    30    5H6M    *    0    0    AGCTAA    *    NM:i:1
> r004    0    ref    16    30    6M14D5M    *    0    0    ATAGCTTCAGC    *
> r003    2064    ref    29    30    6H5M    *    0    0    TAGGC    *    NM:i:0
> r001    147    ref    37    30    9M    =    7    -41    CAGCGGCAT
> *    NM:i:1
>
>
> Which version of samtools is on the $PATH on the test system?
>
> Could the test system have run out of disk space again?
>
> The tests are passing on my local development instance (before
> and after updating to latest galaxy-central), and on TravisCI using
> the latest Galaxy: https://travis-ci.org/peterjc/pico_galaxy/builds/48485673
>
> Thanks,
>
> Peter

Any ideas? Are any of the other tools on either Tool Shed showing
the same error?

Thanks,

Peter
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